There can be various problems in boundary scan testing, such as open circuits in the scan chain, tested device designs not conforming to the boundary scan testing standards, and negative impact of the tested boards. Based on in-depth study of the basic principles of boundary scan and practical engineering experience, it proposed a boundary scan chain testing algorithm. According to the key description information in BSDL file, the algorithm controlled the boundary scan testing system to shift the characteristic data, processed the output data, realized the judgment of the test results, and checked the problems in the chain. The chain testing algorithm can be programmed and is easy to engineering. It has been applied to the actual boundary scan testing to check the chain and improve the testing efficiency.